added a comment - - edited
If you display hidden pages, the Spaces gadgets lists: 'AnnotationCode', 'AppWithinMinutes', 'Blog', 'ColorThemes', 'Dashboard', 'Invitation', 'Main', 'Panels', 'Sandbox', 'Scheduler', 'Stats', 'XWiki'. In this case the Spaces gadgets make sense because it shows all the spaces that exists in XWiki.
Right now on a fresh instance the Spaces gadgets lists: 'Blog', 'Main', 'Sandbox', 'XWiki'.
The Applications panel lists: 'Blog', 'Dashboard', 'User Directory' + links to AppWithinMinutes and Extension Manager.
IMO it shouldn't list 'Blog' because I consider it to be an application, and it shouldn't list 'XWiki' because I actually can't access it and I shouldn't care about it since mostly it contains hidden pages.
It will be left with 'Main' and 'Sandbox' which could be considered Content spaces.
All new spaces created by user that contain normal pages should be listed in the Spaces gadget, all the new applications created by user should be listed in the Applications panel.
This could be one use case and this issue has been created with this use case in mind.
Another use case, the one that you are talking about: 'a filterable Space gadget'. IMO this is very similar to a Favorites gadget.
In the configuration area you should have a list with all the Spaces and with 2 states: 'Show' / 'Hide' (just like for Gmail's Labels).
Initially all the spaces that are hidden will be defaulted to 'Hide', but in some cases the user could override and make visible even some hidden spaces if he wants to.
As JV said this 'Show'/'Hide' option would 'affect' just the Spaces gadget. The spaces and pages will be available and visible (or hidden in the Search, Tree, etc.) accordingly to their Hidden Documents state. Actually right now Hide / Hidden is a bit confusing, so maybe .... in the Space gadget we should have 'Favorite': 'Yes'/'No' instead of 'Show'/'Hide' with the same remarks as above.